Auxin signaling modules regulate maize inflorescence architecture

Galli, Mary; Liu, Qiujie; Moss, Britney L.; Malcomber, Simon T.; Li, Wei; Gaines, Craig; Federici, Silvia; Roshkovan, Jessica; Meeley, Robert B.; Nemhauser, Jennifer L.; Gallavotti, Andrea

doi:10.1073/pnas.1516473112

Cited by 142 publications

(138 citation statements)

References 63 publications

(57 reference statements)

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“…Testing a maize co-ortholog of ARF5 (ZmARF29; Galli et al, 2015) on maize gDNA (Zm-gDNA) by DAP-seq, we observed similar, but not identical, motif spacing preferences with two dominant spacing groups in maize compared to the eight more distributed groups in Arabidopsis ( Figure 6C). To determine if the ZmARF29 protein or the maize gDNA influenced the spacing differences, we assayed ZmARF29 using Arabidopsis gDNA (At-gDNA).…”

Section: Cooperative Binding Of Arf Homodimers At Phased Motif Repeatsmentioning

confidence: 88%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

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SUMMARYThe cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TFspecific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.

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Section: Cooperative Binding Of Arf Homodimers At Phased Motif Repeatsmentioning

confidence: 88%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

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368

482

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“…DII responded to both exogenous IAA applied to leaf pieces and roots as well as endogenous auxin signaling in leaves, roots, and developing tassels. The important role of auxin in maize development (Forestan and Varotto, 2012;Galli et al, 2015;McSteen, 2010;von Behrens et al, 2011;Yu et al, 2016;Zhang et al, 2014) and during the cell cycle (Del Pozo and Manzano, 2014;Himanen et al, 2002) highlights the utility of the DII marker.…”

Section: Discussionmentioning

confidence: 99%

“…In maize (Zea mays), auxin contributes to inflorescence development (Galli et al, 2015), tassel branching (Gallavotti et al, 2008a), and root structure (Jansen et al, 2012;Zhang et al, 2014). The currently available auxin reporter in maize uses the synthetic promoter element DR5 to drive the expression of an endoplasmic reticulum retained Red Fluorescent Protein (DR5rev::mRFP-er, DR5) in response to increased auxin.…”

mentioning

confidence: 99%

A DII Domain-Based Auxin Reporter Uncovers Low Auxin Signaling during Telophase and Early G1

Mir¹,

Aranda²,

Biaocchi

et al. 2016

Plant Physiol.

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A sensitive and dynamically responsive auxin signaling reporter based on the DII domain of the INDOLE-3-ACETIC ACID28 (IAA28, DII) protein from Arabidopsis (Arabidopsis thaliana) was modified for use in maize (Zea mays). The DII domain was fused to a yellow fluorescent protein and a nuclear localization sequence to simplify quantitative nuclear fluorescence signal. DII degradation dynamics provide an estimate of input signal into the auxin signaling pathway that is influenced by both auxin accumulation and F-box coreceptor concentration. In maize, the DII-based marker responded rapidly and in a dose-dependent manner to exogenous auxin via proteasome-mediated degradation. Low levels of DII-specific fluorescence corresponding to high endogenous auxin signaling occurred near vasculature tissue and the outer layer and glume primordia of spikelet pair meristems and floral meristems, respectively. In addition, high DII levels were observed in cells during telophase and early G1, suggesting that low auxin signaling at these stages may be important for cell cycle progression.

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“…Our third marker was the ZmARF4 gene, a close homolog of the Arabidopsis MONOPTEROS (MP) auxin response factor (Hardtke and Berleth, 1998;Galli et al, 2015). ZmARF4 was expressed in the vascular bundles of wild type embryos (Figure 3i).…”

Section: Embryogenesis Of Shai1 Mutantmentioning

confidence: 99%

Autonomous and non‐autonomous functions of the maize Shohai1 gene, encoding a RWP‐RK putative transcription factor, in regulation of embryo and endosperm development

Mimura

Kudo

et al. 2018

The Plant Journal

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In plants, establishment of the basic body plan during embryogenesis involves complex processes of axis formation, cell fate specification and organ differentiation. While molecular mechanisms of embryogenesis have been well studied in the eudicot Arabidopsis, only a small number of genes regulating embryogenesis has been identified in grass species. Here, we show that a RKD-type RWP-RK transcription factor encoded by Shohai1 (Shai1) is indispensable for embryo and endosperm development in maize. Loss of Shai1 function causes variable morphological defects in the embryo including small scutellum, shoot axis bifurcation and arrest during early organogenesis. Analysis of molecular markers in mutant embryos reveals disturbed patterning of gene expression and altered polar auxin transport. In contrast with typical embryo-defective (emb) mutants that expose a vacant embryo pocket in the endosperm, the endosperm of shai1 kernels conforms to the varied size and shape of the embryo. Furthermore, genetic analysis confirms that Shai1 is required for autonomous formation of the embryo pocket in endosperm of emb mutants. Analyses of genetic mosaic kernels generated by B-A translocation revealed that expression of Shai1 in the endosperm could partially rescue a shai1 mutant embryo and suggested that Shai1 is involved in non-cell autonomous signaling from endosperm that supports normal embryo growth. Taken together, we propose that the Shai1 gene functions in regulating embryonic patterning during grass embryogenesis partly by endosperm-to-embryo interaction.

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Auxin signaling modules regulate maize inflorescence architecture

Cited by 142 publications

References 63 publications

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

A DII Domain-Based Auxin Reporter Uncovers Low Auxin Signaling during Telophase and Early G1

Autonomous and non‐autonomous functions of the maize Shohai1 gene, encoding a RWP‐RK putative transcription factor, in regulation of embryo and endosperm development

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